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Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Enterococcus faecalis V583
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 289 0.2M MgCl2, 0.1M HEPES, 30% PEG 400, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.43 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.209 α = 90 b = 55.179 β = 95.63 c = 140.387 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Mirrors 2007-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97948 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 46 97.7 0.15 13.8 4 51845 51845
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 83.9 0.563 1.63 2.4 2211
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.95 45.83 49205 49205 2616 97.42 0.20364 0.20364 0.20131 0.2023 0.24845 0.2479 RANDOM 30.741
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.09 0.06 -0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.843 r_dihedral_angle_4_deg 20.353 r_dihedral_angle_3_deg 15.903 r_dihedral_angle_1_deg 6.285 r_scangle_it 3.26 r_scbond_it 1.981 r_angle_refined_deg 1.464 r_mcangle_it 1.049 r_mcbond_it 0.731 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.843 r_dihedral_angle_4_deg 20.353 r_dihedral_angle_3_deg 15.903 r_dihedral_angle_1_deg 6.285 r_scangle_it 3.26 r_scbond_it 1.981 r_angle_refined_deg 1.464 r_mcangle_it 1.049 r_mcbond_it 0.731 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.275 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4810 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELXD phasing MLPHARE phasing DM phasing RESOLVE phasing HKL-3000 phasing